Journal: Scientific Reports

Article Title: Decoding herbal materials of TCM preparations with the multi-barcode sequencing approach

doi: 10.1038/s41598-022-09979-z

Figure Lengend Snippet: The distribution of prescribed herbal species (PHS) detected in each sample from NJW and DHW preparations. ( A ) The detected PHS in NJW samples based on ITS2; ( B ) The detected PHS in NJW samples based on trnL ; ( C ) The detected PHS in DHW samples based on ITS2; ( D ) The detected PHS in DHW samples based on trnL. Note that each column represents a sample, and each row represents a PHS. In the heatmap that was drawn in R (version 3.5.2) package “pheatmap” ( https://cran.rstudio.com/web/packages/pheatmap/index.html ), the color represents the relative abundance of PHS (normalized according to column) detected in this sample. The number “1” represents the PHS that was detected in this sample, while “0” represents the PHS that was not detected.

Article Snippet: As for the composition of PHS, we used the heatmap with gradient color using R (version 3.5.2) package “pheatmap” ( https://cran.rstudio.com/web/packages/pheatmap/index.html ) to illustrate the composition of the PHS based on their relative abundance in each sample, and used 0 (not detected) and 1 (detected) to describe the existence status of PHS in each sample.

Techniques:

Journal: Scientific Reports

Article Title: Decoding herbal materials of TCM preparations with the multi-barcode sequencing approach

doi: 10.1038/s41598-022-09979-z

Figure Lengend Snippet: Comparison of the similarity of all DHW samples from intra-/inter-manufacturers based on prescribed herbal materials using Euclidean distances. Heatmap clusters displayed the distance of all samples based on the existence of prescribed herbal species using hierarchical clustering, and network clusters illustrated these differences based on ITS2 ( A , B ) and trnL ( C , D ) sequencing results, respectively. For heatmap ( A , C ), which was drawn in R (version 3.5.2) package “pheatmap” ( https://cran.rstudio.com/web/packages/pheatmap/index.html ), the gradient color bars mean the distance between any two samples, while the red and the blue color depicts the two extreme distances between samples. For network ( B , D ) that was visualized in Cytoscape (version 3.7.1; https://cytoscape.org/ ), each edge represents the distance of any two samples with a distance less than or equal to 5.0 for ITS2 and 4.2 for trnL .

Article Snippet: As for the composition of PHS, we used the heatmap with gradient color using R (version 3.5.2) package “pheatmap” ( https://cran.rstudio.com/web/packages/pheatmap/index.html ) to illustrate the composition of the PHS based on their relative abundance in each sample, and used 0 (not detected) and 1 (detected) to describe the existence status of PHS in each sample.

Techniques: Comparison, Sequencing